What version of tleap are you using? The intrinsic GB radii section has
been written in topology files as long as I can remember.
It may help to put in a command like
set default pbradii mbondi2
or something like that (whichever PBRadii you want to use) into your script
before you write the topology files. This should add the radii information
for you.
HTH,
Jason
On Wed, Feb 29, 2012 at 7:32 AM, g t <sketchfoot.gmail.com> wrote:
> Hi,
>
> I am trying to run an mmpbsa calculation using the perl script. I have
> created the input topology files for complex, ligand and receptor. However
> upon submission the job does not complete properly. The error I have been
> able to find is in the file X_ThX_Complex_com.pdb.1:
>
> ERROR: Flag "RADII" not found in PARM file
>
> If I load my parm files into ptraj i also get the following errors related
> to the generalised born intrinsic dielectric radii:
>
> PRMTOP does not contain %FLAG RADIUS_SET
> PRMTOP does not contain %FLAG RADII
> PRMTOP does not contain %FLAG SCREEN
>
> The following is an example set-up file I use to create the parm files. Is
> there a command I am missing that sets the radii?
>
> ##########
> source leaprc.gaff
> source leaprc.ff03.r1
> loadoff all_aminoct02.lib
> loadoff ${dirNo}_final.lib
> mol = loadpdb ${dirNo}_complex_unsolvated.pdb
> bond mol.64.SG mol.157.SG
> solvatebox mol TIP3PBOX 10.0
> charge mol
> #addions2 mol K+ 14.0
> #savepdb mol ${dirNo}_complex_SOLVATED.pdb
> saveamberparm mol dehydrated2a_${dirNo}.parm dehydrated2a_${dirNo}.crd
> (i later use rdparm to strip out the water molecules to create the
> dehydrated complex)
> #######
>
> Any help would be greatly appreciated.
>
> Best regards,
> ET
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 29 2012 - 14:00:02 PST
